The idea of a mother finding her own children stupid and tiresome seems pretty "out there" in Austen's world. Usually OTHER characters are annoyed by children, while the good moms are nurturing and the "bad" moms are excessively doting and indulgent (like Mrs. Bennett, or Lady Middleton). Lady Catherine's daughter IS stupid and tiresome, but Lady Catherine thinks she's a paragon.

The only mother who seems negligent and less than enchanted with her own children is Mary Musgrove in Persuasion, and that's a symptom of her narcissistic, irritable character. I don't picture Charlotte as over-indulgent or narcissistic.

Austen gives examples of children taking after either parent, so it's possible that the junior Collinses could take after their dad rather than Charlotte... but it seems to me that Charlotte has taken charge of many aspects of her domestic situation and contrives to keep Mr. Collins at a distance from the center of home life. She seems to have the house pretty much to herself. So I can more easily see her as the "primary parent," raising the kids to be pleasing companions to herself.